LAMMPS (23 Jun 2022)
# solvated ubiquitin molecule with AMOEBA force field

units           real
boundary        p p p
atom_modify     sort 0 0.0

atom_style      amoeba

bond_style      class2
angle_style     amoeba
dihedral_style  fourier
improper_style  amoeba

# per-atom properties required by AMOEBA or HIPPO

fix             amtype all property/atom i_amtype ghost yes
fix             extra all property/atom i_amgroup d_redID d_pval ghost yes
fix             extra2 all property/atom i_polaxe d2_xyzaxis 3

fix             pit all amoeba/pitorsion
fix_modify      pit energy yes
fix             bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify      bit energy yes

# read data file

read_data       data.ubiquitin fix amtype NULL "Tinker Types"                 fix pit "pitorsion types" "PiTorsion Coeffs"                 fix pit pitorsions PiTorsions                 fix bit bitorsions BiTorsions
Reading data file ...
  orthogonal box = (0 0 0) to (54.99 41.91 41.91)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  9737 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  3 = max impropers/atom
  reading bonds ...
  6908 bonds
  reading angles ...
  5094 angles
  reading dihedrals ...
  3297 dihedrals
  reading impropers ...
  651 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     9 = max # of 1-3 neighbors
    19 = max # of 1-4 neighbors
    21 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.072 seconds

pair_style      amoeba
pair_coeff      * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05
Skipping section:   AMOEBA Protein Force Field Atom Classes  
Skipping section:   Torsion-Torsion Parameters  
Skipping section:   Biopolymer Atom Type Conversions  
Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05

special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0.5      0.5      0.5     
  special bond factors coul:  0.5      0.5      0.5     
     4 = max # of 1-2 neighbors
     9 = max # of 1-3 neighbors
    19 = max # of 1-4 neighbors
    58 = max # of 1-5 neighbors
    21 = max # of special neighbors
  special bonds CPU = 0.002 seconds

# thermo output

compute         virial all pressure NULL virial

thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]

#dump            1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify     1 sort id

# dynamics

fix            1 all nve

thermo         1
run            10
AMOEBA force field settings
  hal: cut 12 taper 10.8 vscale 0 0 1 1
  multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
  polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
         pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
  precondition: cut 4.5
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 8 6 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair amoeba, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  AMOEBA group count: 3196
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes
   Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
         0   0             -35338.057      2856.5938      1955.5431      224.37609      65.00809       5101.5211     -30247.585     -6336.5196     -5795.4272     -6329.8149     -6884.3167      349.52657      77.164877      652.41925    
         1   29.61379      -35356.153      2037.3541      1840.7883      223.90217      64.293945      4166.3385     -30341.522     -6486.773      -6452.8463     -6841.5982     -7386.1106      311.38025      120.72605      545.35513    
         2   78.518242     -35383.65       825.39919      1538.3909      222.55095      62.191009      2648.5321     -30467.814     -5502.9841     -6410.2998     -6396.1829     -6937.8137      217.3515       210.76948      294.28051    
         3   88.8921       -35402.11       938.99299      1162.2914      220.5271       58.832521      2380.644      -30453.516     -1929.5417     -3331.1291     -2769.7218     -3350.5733      117.32302      279.72705      31.237776    
         4   68.740402     -35477.589      2048.0659      858.03795      218.14277      54.460022      3178.7066     -30316.325      2041.1138      594.25938      1665.7799      1030.8539      66.230421      304.28296     -155.80224    
         5   76.267862     -35707.869      2206.6534      736.37385      215.75693      49.401674      3208.1859     -30299.377      2276.9276      536.21124      1893.4621      1258.492       92.097191      299.65604     -228.58369    
         6   118.24373     -36092.77       1166.179       815.59206      213.67399      44.022297      2239.4673     -30435.629     -1677.8051     -3988.2428     -2669.6848     -3247.7207      197.42472      285.87129     -162.35459    
         7   137.7204      -36521.444      782.87113      1026.745       212.04289      38.686259      2060.3452     -30479.082     -5987.83       -8386.8104     -7363.188      -7888.261       357.00835      253.66346      32.827786    
         8   112.66452     -36897.181      1750.0569      1269.152       210.83571      33.742799      3263.7874     -30379.432     -7886.4081     -9703.2601     -9043.015      -9555.2908      490.76046      182.31259      278.727      
         9   88.237359     -37209.906      2695.1766      1454.55        209.91331      29.503458      4389.1434     -30276.565     -8202.16       -9492.368      -9110.7037     -9639.2288      502.55699      107.82333      443.6705     
        10   108.86756     -37474.988      2240.4603      1523.7936      209.10313      26.208515      3999.5656     -30333.279     -8468.4347     -9956.923      -9709.5874     -10224.682      365.98214      95.262991      425.12746    
Loop time of 6.03244 on 4 procs for 10 steps with 9737 atoms

Performance: 0.143 ns/day, 167.568 hours/ns, 1.658 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads

AMOEBA timing breakdown:
  Init    time: 0.0192504      0.32%
  Hal     time: 1.86975       31.05%
  Mpole   time: 0.633256      10.52%
  Induce  time: 2.26029       37.54%
  Polar   time: 1.23884       20.57%
  Total   time: 6.02139     

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.0202     | 6.0215     | 6.0228     |   0.0 | 99.82
Bond    | 0.0029895  | 0.0033805  | 0.0036579  |   0.4 |  0.06
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0044978  | 0.0059188  | 0.0070446  |   1.5 |  0.10
Output  | 0.00055049 | 0.00062352 | 0.00079826 |   0.0 |  0.01
Modify  | 0.00067451 | 0.00071394 | 0.00074612 |   0.0 |  0.01
Other   |            | 0.0003294  |            |       |  0.01

Nlocal:        2434.25 ave        2498 max        2390 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost:        16683.2 ave       16765 max       16568 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs:    1.40982e+06 ave 1.52088e+06 max 1.30717e+06 min
Histogram: 2 0 0 0 0 0 0 0 1 1

Total # of neighbors = 5639296
Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:07
